Samantha M. Hurndon Week 12: DNA Microarray project

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  1. From the methods section of your microarray paper, you need to figure out the following:
    • What samples did they collect and use for the microarray experiment?
    • How many microarray chips did they hybridize in the experiment?
    • Which samples were paired to hybridize on the chip?
    • Which was labeled red (Cy5)? Which was labeled green (Cy3)?
    • How many replicates did they perform of each type?
      • Biological replicates are made from entirely different biological samples.
      • Technical replicates are made when one biological sample is split at a particular stage in the procedure and then carried through to the end of the procedure.
  2. Record this information on your individual journal pages. If you have this from your journal outline, you can copy and paste it into your new journal page.
  3. Using the sdrf.xls file, you need to then find the names of the files that correspond to the names of your samples from the paper. Make a list that says which file corresponds to which sample.
  4. The instructor will then show you which columns of data to copy into a new Master spreadsheet. You will upload this spreadsheet to the wiki and then link to it from your journal page.

Master Spreadsheet for Week 13 Lab

H_pylori_Master_20111130_KD.xls

Link to all files from Douillard paper

http://www.ebi.ac.uk/arrayexpress/files/E-BUGS-78

Readme's

Processed

Raw

.sdrf.txt file

Array Files

Cy5

  • hp0906KO total RNA (C1)
MBAD_32063.txt
  • CCUG17874 total RNA (C1)
MBAD_32085.txt
  • hp0906KO total RNA (B1)
MBAD_32065.txt
  • hp0906KO total RNA (A1)
MBAD_32067.txt
  • hp0958 KO total RNA (B1)
MBAD_32059.txt
  • hp0958 KO total RNA (A1)
MBAD_32057.txt
  • CCUG17874 total RNA (B1)
MBAD_32075.txt
  • CCUG17874 total RNA (A1)
MBAD_32081.txt
  • hp0958 KO total RNA (C1)
MBAD_32055.txt
  • CCUG17874 gDNA (B1)
MBAD_32069.txt
  • CCUG17874 gDNA (A1)__bugs.sgul.ac.uk:BuG@Sbase/BioSample:23772
MBAD_32081.txt

Cy3

  • CCUG17874 gDNA (A3)
MBAD_32062.txt
  • CCUG17874 gDNA (A3)__bugs.sgul.ac.uk:BuG@Sbase/BioSample:23768
MBAD_32084.txt
  • CCUG17874 gDNA (A2)
MBAD_32064.txt
  • CCUG17874 gDNA (A1)
MBAD_32067.txt
  • NCTC26695 gDNA (B1)
MBAD_32074.txt
  • CCUG17874 gDNA (A5)__bugs.sgul.ac.uk:BuG@Sbase/BioSample:23768
MBAD_32058.txt
  • NCTC26695 gDNA (A1)
MBAD_32070.txt
  • CCUG17874 gDNA (A4)__bugs.sgul.ac.uk:BuG@Sbase/BioSample:23768
MBAD_32056.txt
  • CCUG17874 gDNA (A2)__bugs.sgul.ac.uk:BuG@Sbase/BioSample:23768
MBAD_32068.txt
  • CCUG17874 gDNA (A1)__bugs.sgul.ac.uk:BuG@Sbase/BioSample:23768
MBAD_32080.txt
  • CCUG17874 gDNA (A6)__bugs.sgul.ac.uk:BuG@Sbase/BioSample:23768
MBAD_32054.txt

Hybridizations

  • Cy5 hp0906KO (C1) with Cy3 CCUG17874 (A3) → Hyb:32525
  • Cy3 CCUG17874 (A3)-23856 with Cy5 CCUG17874 (C1) → Hyb:32519
  • Cy5 hp0906KO (B1) with Cy3 CCUG17874 (A2) → Hyb:32524
  • Cy3 CCUG17874 (A1) with Cy5 hp0906KO (A1) → Hyb:32523
  • Cy5 CCUG17874 (B1) with Cy3 NCTC26695 (B1) → Hyb:32528
  • Cy3 CCUG17874 (A5) with Cy5 hp0958 KO (B1) → Hyb:32521
  • Cy3 NCTC26695 (A1) with Cy5 CCUG17874 (A1) → Hyb:32526
  • Cy5 hp0958 KO (A1) with Cy3 CCUG17874 (A4) → Hyb:32520
  • Cy3 CCUG17874 (A2)-23855 with Cy5 CCUG17874 (B2)-23817 → Hyb:35218
  • Cy3 CCUG17874 (A1)-23769 with Cy5 CCUG17874 (A1)-23814 → Hyb:32517
  • Cy3 CCUG17874 (A6) with Cy5 hp0958 KO (C1) → Hyb:32522


BIOL368/F11:Week_12

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